The xel'naga cut the Khalis and Uraj crystals from a monolithic khaydarin crystal and gave them to the protoss. The Sargas Tribe was entrusted with Khalis and over time the crystal's properties diverged from those of Uraj. Most of the protoss rejecting the Khala, and who formed the Rogue Tribes, came from the Sargas. As a result Khalis took on the energies associated with the Rogues. When the Rogues were banished from Aiur and became the Dark Templar, they took Khalis with them. This appropriation was discovered only belatedly by the Khalai.[1]

The Dark Templar tracked the zerg to Char and chose to test themselves against small groups of zerg. The zerg proved frighteningly resilient and numerous and the protoss brought Khalis to Char intending to wield the crystal's energies against the zerg. After some success the protoss were overwhelmed by the Overmind's massive counterattack and Khalis was lost to the zerg. The crystal was left behind on Char when the Swarm went to invade Aiur.[1]

When the cerebrates merged together to form a new Overmind, they locked onto the Khalis' energies and nested near it.[2]

A protoss army led by PraetorArtanis, Zeratul, and the Executor returned to Char to retrieve the Khalis with the assistance of Sarah Kerrigan, who suggested striking directly for the crystal and escaping before the zerg could muster in strength. Artanis preferred a bold alternative whereas they would strike and weaken the Overmind, pacifying the local zerg long enough to extract the crystal. Either was feasible given the circumstances. The protoss struck into the nesting area and retrieved Khalis.[2]

The protoss returned to Shakuras with the crystals. Zeratul carried the Khalis into the xel'naga temple[3] and inserted the crystal into the structure's mechanisms. The temple's activation created a giant energy burst that scoured the zerg from the planet.[4]